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Coexpression cluster:C136: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 10:40, 17 September 2013


Full id: C136_Wilms_extraskeletal_anaplastic_rhabdomyosarcoma_cholangiocellular_nonsmall_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr10:110407997..110408002,+p@chr10:110407997..110408002
+
Hg19::chr10:123491370..123491379,-p@chr10:123491370..123491379
-
Hg19::chr10:21291623..21291629,-p@chr10:21291623..21291629
-
Hg19::chr10:22640320..22640328,+p@chr10:22640320..22640328
+
Hg19::chr10:29612487..29612499,+p@chr10:29612487..29612499
+
Hg19::chr10:29612546..29612580,+p@chr10:29612546..29612580
+
Hg19::chr10:29613031..29613036,+p@chr10:29613031..29613036
+
Hg19::chr10:29613050..29613060,+p@chr10:29613050..29613060
+
Hg19::chr10:29643287..29643316,+p@chr10:29643287..29643316
+
Hg19::chr10:52612862..52612869,+p@chr10:52612862..52612869
+
Hg19::chr10:54010532..54010547,+p@chr10:54010532..54010547
+
Hg19::chr10:54010561..54010562,+p@chr10:54010561..54010562
+
Hg19::chr10:54010629..54010641,+p@chr10:54010629..54010641
+
Hg19::chr10:54010664..54010675,+p@chr10:54010664..54010675
+
Hg19::chr10:54011381..54011388,+p@chr10:54011381..54011388
+
Hg19::chr10:54373384..54373394,-p@chr10:54373384..54373394
-
Hg19::chr10:54380431..54380438,-p@chr10:54380431..54380438
-
Hg19::chr10:54380494..54380526,-p@chr10:54380494..54380526
-
Hg19::chr10:54434202..54434206,+p@chr10:54434202..54434206
+
Hg19::chr10:54435392..54435398,+p@chr10:54435392..54435398
+
Hg19::chr10:54464025..54464030,+p@chr10:54464025..54464030
+
Hg19::chr10:95575127..95575132,+p@chr10:95575127..95575132
+
Hg19::chr10:95579364..95579367,-p@chr10:95579364..95579367
-
Hg19::chr11:111405448..111405452,-p@chr11:111405448..111405452
-
Hg19::chr11:44359184..44359192,-p@chr11:44359184..44359192
-
Hg19::chr11:84534461..84534473,-p@chr11:84534461..84534473
-
Hg19::chr11:9879819..9879831,-p@chr11:9879819..9879831
-
Hg19::chr11:9879844..9879867,-p@chr11:9879844..9879867
-
Hg19::chr12:47578884..47578898,-p@chr12:47578884..47578898
-
Hg19::chr12:47686521..47686535,-p@chr12:47686521..47686535
-
Hg19::chr12:54651945..54651977,-p10@CBX5
Hg19::chr12:54651996..54652005,-p52@CBX5
Hg19::chr12:65915374..65915386,-p@chr12:65915374..65915386
-
Hg19::chr12:66414428..66414436,-p@chr12:66414428..66414436
-
Hg19::chr14:54712704..54712709,-p@chr14:54712704..54712709
-
Hg19::chr14:57540809..57540853,-p@chr14:57540809..57540853
-
Hg19::chr14:57618195..57618202,+p@chr14:57618195..57618202
+
Hg19::chr14:68282778..68282790,-p2@ZFYVE26
Hg19::chr14:68282796..68282809,-p3@ZFYVE26
Hg19::chr14:68282823..68282830,-p6@ZFYVE26
Hg19::chr14:68283075..68283091,-p7@ZFYVE26
Hg19::chr14:68283125..68283137,-p5@ZFYVE26
Hg19::chr15:26342640..26342684,+p@chr15:26342640..26342684
+
Hg19::chr15:27111637..27111644,+p20@GABRA5
Hg19::chr15:35280823..35280852,-p6@ZNF770
Hg19::chr15:35280863..35280908,-p3@ZNF770
Hg19::chr15:67665298..67665308,-p@chr15:67665298..67665308
-
Hg19::chr16:25157665..25157701,-p9@LOC100506655
Hg19::chr16:25160074..25160087,-p5@LOC100506655
Hg19::chr16:25160169..25160182,-p7@LOC100506655
Hg19::chr16:83715826..83715852,-p@chr16:83715826..83715852
-
Hg19::chr16:83842046..83842058,+p@chr16:83842046..83842058
+
Hg19::chr16:83842085..83842095,+p@chr16:83842085..83842095
+
Hg19::chr16:83842136..83842184,+p@chr16:83842136..83842184
+
Hg19::chr18:22253484..22253496,+p@chr18:22253484..22253496
+
Hg19::chr18:3411569..3411590,+p43@TGIF1
Hg19::chr18:3411595..3411600,+p62@TGIF1
Hg19::chr18:3412005..3412009,+p49@TGIF1
Hg19::chr19:28480060..28480096,-p@chr19:28480060..28480096
-
Hg19::chr19:28480120..28480153,-p@chr19:28480120..28480153
-
Hg19::chr19:43519486..43519516,-p@chr19:43519486..43519516
-
Hg19::chr19:43821388..43821391,-p@chr19:43821388..43821391
-
Hg19::chr19:43866447..43866456,+p@chr19:43866447..43866456
+
Hg19::chr1:107328618..107328622,-p@chr1:107328618..107328622
-
Hg19::chr1:107495934..107495947,+p@chr1:107495934..107495947
+
Hg19::chr1:107495972..107495982,+p@chr1:107495972..107495982
+
Hg19::chr1:874649..874655,+p20@SAMD11
Hg19::chr1:99904362..99904371,-p@chr1:99904362..99904371
-
Hg19::chr21:30202677..30202680,+p@chr21:30202677..30202680
+
Hg19::chr22:49752643..49752667,-p@chr22:49752643..49752667
-
Hg19::chr22:49768853..49768884,+p@chr22:49768853..49768884
+
Hg19::chr22:49769834..49769843,+p@chr22:49769834..49769843
+
Hg19::chr22:49769867..49769888,+p@chr22:49769867..49769888
+
Hg19::chr22:49769903..49769910,+p@chr22:49769903..49769910
+
Hg19::chr22:49769966..49769971,+p@chr22:49769966..49769971
+
Hg19::chr22:50024141..50024142,+p@chr22:50024141..50024142
+
Hg19::chr2:178466057..178466072,+p@chr2:178466057..178466072
+
Hg19::chr2:178467784..178467793,+p2@ENST00000357045
Hg19::chr2:178467806..178467810,+p4@ENST00000357045
Hg19::chr2:178467811..178467821,+p1@ENST00000357045
Hg19::chr2:232030419..232030426,+p@chr2:232030419..232030426
+
Hg19::chr2:232030447..232030460,+p@chr2:232030447..232030460
+
Hg19::chr2:232030473..232030487,+p@chr2:232030473..232030487
+
Hg19::chr2:40548784..40548802,-p@chr2:40548784..40548802
-
Hg19::chr2:40680676..40680690,-p6@SLC8A1
Hg19::chr3:115827500..115827509,-p@chr3:115827500..115827509
-
Hg19::chr3:128208278..128208291,+p4@ENST00000473958
Hg19::chr3:154361030..154361048,-p@chr3:154361030..154361048
-
Hg19::chr4:124464955..124464980,+p@chr4:124464955..124464980
+
Hg19::chr4:4544047..4544060,-p3@STX18
Hg19::chr4:4544061..4544075,-p4@STX18
Hg19::chr4:65591752..65591762,+p@chr4:65591752..65591762
+
Hg19::chr4:65591771..65591789,+p@chr4:65591771..65591789
+
Hg19::chr4:65591798..65591800,+p@chr4:65591798..65591800
+
Hg19::chr5:74322467..74322473,-p@chr5:74322467..74322473
-
Hg19::chr5:74349970..74349983,-p@chr5:74349970..74349983
-
Hg19::chr5:74350271..74350287,-p@chr5:74350271..74350287
-
Hg19::chr5:74352282..74352286,-p@chr5:74352282..74352286
-
Hg19::chr5:75919142..75919153,-p5@F2RL2
Hg19::chr5:75919253..75919269,-p4@F2RL2
Hg19::chr5:92111748..92111752,-p@chr5:92111748..92111752
-
Hg19::chr5:92112305..92112313,-p@chr5:92112305..92112313
-
Hg19::chr6:104996260..104996271,-p@chr6:104996260..104996271
-
Hg19::chr6:104996342..104996353,-p@chr6:104996342..104996353
-
Hg19::chr6:122147424..122147433,+p@chr6:122147424..122147433
+
Hg19::chr6:57381063..57381070,-p@chr6:57381063..57381070
-
Hg19::chr7:135697276..135697294,+p@chr7:135697276..135697294
+
Hg19::chr7:135697298..135697309,+p@chr7:135697298..135697309
+
Hg19::chr7:135697397..135697402,+p@chr7:135697397..135697402
+
Hg19::chr7:151433200..151433217,-p31@PRKAG2
Hg19::chr7:25331046..25331057,+p@chr7:25331046..25331057
+
Hg19::chr7:25708292..25708320,-p@chr7:25708292..25708320
-
Hg19::chr7:25878694..25878698,+p@chr7:25878694..25878698
+
Hg19::chr7:25886548..25886557,+p@chr7:25886548..25886557
+
Hg19::chr8:105235398..105235417,+p28@RIMS2
Hg19::chr8:105235550..105235571,+p11@RIMS2
Hg19::chr8:105235572..105235610,+p4@RIMS2
Hg19::chr8:105235613..105235625,+p25@RIMS2
Hg19::chr8:105235707..105235716,+p18@RIMS2
Hg19::chr8:105360173..105360177,+p@chr8:105360173..105360177
+
Hg19::chr8:105375900..105375904,-p@chr8:105375900..105375904
-
Hg19::chr8:115798994..115799001,+p@chr8:115798994..115799001
+
Hg19::chr8:127409534..127409543,+p@chr8:127409534..127409543
+
Hg19::chr8:127434688..127434698,+p@chr8:127434688..127434698
+
Hg19::chr8:127514281..127514286,+p@chr8:127514281..127514286
+
Hg19::chr8:95333973..95333982,+p@chr8:95333973..95333982
+
Hg19::chr9:129376456..129376465,+p5@LMX1B
Hg19::chr9:3734564..3734569,+p1@BC047388
Hg19::chr9:81579274..81579286,+p@chr9:81579274..81579286
+
Hg19::chr9:9972816..9972821,-p@chr9:9972816..9972821
-
Hg19::chrX:132090091..132090097,+p@chrX:132090091..132090097
+
Hg19::chrX:132092649..132092662,-p12@HS6ST2
Hg19::chrX:13469109..13469118,+p@chrX:13469109..13469118
+
Hg19::chrY:18183164..18183170,+p@chrY:18183164..18183170
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
kidney4.34e-0926
kidney mesenchyme4.34e-0926
upper urinary tract4.34e-0926
kidney rudiment4.34e-0926
kidney field4.34e-0926
cavitated compound organ7.41e-0831


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.11.24138e-12
MA0004.10.715591
MA0006.10.086095
MA0007.10.113
MA0009.10.438337
MA0014.11.49586e-07
MA0017.10.471408
MA0019.10.278752
MA0024.10.114721
MA0025.10.103186
MA0027.11.3181
MA0028.10.000497354
MA0029.10.128256
MA0030.10.0290138
MA0031.10.0799094
MA0038.10.999293
MA0040.10.0327271
MA0041.10.0408779
MA0042.10.0264672
MA0043.10.0537497
MA0046.10.419958
MA0048.10.0112601
MA0050.10.208075
MA0051.10.192455
MA0052.12.83026
MA0055.10.02362
MA0056.10
MA0057.10.0083444
MA0058.10.315858
MA0059.10.438807
MA0060.11.94594
MA0061.10.00720032
MA0063.10
MA0066.12.39785
MA0067.10.199375
MA0068.10.00281717
MA0069.10.413533
MA0070.10.395123
MA0071.11.35348
MA0072.10.688548
MA0073.13.88624e-14
MA0074.10.717758
MA0076.10.000492309
MA0077.10.0428262
MA0078.10.215788
MA0081.10.131553
MA0083.11.19788
MA0084.10.324478
MA0087.10.68245
MA0088.10.00387172
MA0089.10
MA0090.10.029392
MA0091.10.95558
MA0092.10.263664
MA0093.10.907658
MA0095.10
MA0098.10
MA0100.10.014674
MA0101.10.230448
MA0103.10.26956
MA0105.10.0289212
MA0106.10.0201131
MA0107.10.0392762
MA0108.20.641573
MA0109.10
MA0111.10.0753842
MA0113.10.0239853
MA0114.10.0964326
MA0115.11.47245
MA0116.10.0113816
MA0117.10.233846
MA0119.10.855246
MA0122.10.260087
MA0124.11.34112
MA0125.10.316678
MA0130.10
MA0131.11.27858
MA0132.10
MA0133.10
MA0135.10.22675
MA0136.10.540976
MA0139.16.54842e-06
MA0140.11.65618
MA0141.10.959203
MA0142.10.56224
MA0143.10.489926
MA0144.10.656154
MA0145.10.000443691
MA0146.12.41802e-09
MA0147.10.456231
MA0148.11.09417
MA0149.10.00612325
MA0062.24.22233e-05
MA0035.21.04221
MA0039.22.73221e-10
MA0138.20.385549
MA0002.20.0970797
MA0137.20.192107
MA0104.20.323585
MA0047.21.84924
MA0112.20.227356
MA0065.20.00623681
MA0150.10.555456
MA0151.10
MA0152.11.70882
MA0153.10.297794
MA0154.10.00091224
MA0155.10.00354398
MA0156.10.126748
MA0157.10.286703
MA0158.10
MA0159.10.350011
MA0160.11.19298
MA0161.10
MA0162.12.39303e-09
MA0163.16.24836e-06
MA0164.10.328805
MA0080.20.0265755
MA0018.20.147066
MA0099.20.598793
MA0079.20
MA0102.20.351955
MA0258.11.63095
MA0259.10.0913268
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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